AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i123_Daunorubicin_Resistance_Pump_aful_reg_300.orf -o123_aful_300.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -x5 -e 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RAG50240	202	Archaeoglobus_fulgidus

Motif number 1

TTAAATACGGGCTCGACGGGATTTGAACCC	1	27	1	GCTCGACGGG	    0.998447	-176
TTGAACCCGCGACCGACGGGTTAAAAGCCC	1	49	1	GACCGACGGG	    0.999166	-154
CAGCCAGGCAGAGCGACGGGCTTTTAACCC	1	66	0	GAGCGACGGG	    0.999548	-137
CTGCCTGGCTGAGCTACGAGCCCTCATCCA	1	85	1	GAGCTACGAG	    0.994707	-118
GTGCATTCGAGATTTGCGGGGAAAAGGC  	1	185	1	GATTTGCGGG	    0.982057	-18
          **********

Masking position 7
Map Score:   12.284

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 44
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

CGTCGGTCGCGGGTTCAAATCCCGTCGAGCC	1	36	0	GGGTTAAATC	    0.992041	-167
CGCGACCGACGGGTTAAAAGCCCGTCGCTCT	1	56	1	GGGTTAAAGC	    0.994097	-147
TAATGGATGAGGGCTCGTAGCTCAGCCAGGC	1	87	0	GGGCTGTAGC	     0.97979	-116
GCGATGGTGAGGATTTAAATCTTTTTCGTGC	1	118	1	GGATTAAATC	     0.97672	-85
CGAGATTTGCGGGGAAAAGGC          	1	192	1	GGGGAAAGGC	     0.97977	-11
          ***** *****

Masking position 2
Map Score:   4.62967

Number of sites scoring better than the average of aligned sites = 224
Number in coding regions = 194
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 3

GGCTTTTAACCCGTCGGTCGCGGGTTCAAATC	1	46	0	CCGTCGTGCG	    0.989384	-157
AAGCCCGTCGCTCTGCCTGGCTGAGCTACGAG	1	73	1	CTCTGCTGCT	    0.996321	-130
GATTTAAATCCTCACCATCGCTAATGGATGAG	1	107	0	CTCACCTGCT	    0.996541	-96
ATAAATATATCTGTCCTTTGCTTGTATCTTTA	1	151	0	CTGTCCTGCT	    0.998629	-52
          ****** * ***

Masking position 8
Map Score:   1.74428

Number of sites scoring better than the average of aligned sites = 64
Number in coding regions = 62
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

CGGGCTCGACGGGATTTGAACCCGCGACCGA	1	34	1	GGGATTTAAC	    0.983922	-169
GCAGAGCGACGGGCTTTTAACCCGTCGGTCG	1	58	0	GGGCTTTAAC	    0.996879	-145
TAATGGATGAGGGCTCGTAGCTCAGCCAGGC	1	87	0	GGGCTCGAGC	    0.985955	-116
AATCTTTTTCGTGCTCTAAAGATACAAGCAA	1	135	1	GTGCTCTAAG	    0.990601	-68
ATATTTATCGGTGCATTCGAGATTTGCGGGG	1	175	1	GTGCATTGAG	    0.930391	-28
          ******* ***

Masking position 3
Map Score:   2.38485

Number of sites scoring better than the average of aligned sites = 337
Number in coding regions = 315
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 5

AGCTCAGCCAGGCAGAGCGACGGGCTTTTA	1	70	0	GGCAGAGCGA	     0.99756	-133
CGCTCTGCCTGGCTGAGCTACGAGCCCTCA	1	81	1	GGCTGAGCTA	    0.996388	-122
ACAAGCAAAGGACAGATATATTTATCGGTG	1	158	1	GACAGATATA	    0.959941	-45
          **********

Masking position 6
Map Score:   0.863347

Number of sites scoring better than the average of aligned sites = 117
Number in coding regions = 107
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 6

CTTTAGAGCACGAAAAAGATTTAAATCCTC	1	126	0	CGAAAAAGAT	    0.990748	-77
CTTTTTCGTGCTCTAAAGATACAAGCAAAG	1	138	1	CTCTAAAGAT	    0.980335	-65
TCGAATGCACCGATAAATATATCTGTCCTT	1	165	0	CGATAAATAT	     0.98566	-38
          **********

Masking position 5
Map Score:   0.81895

Number of sites scoring better than the average of aligned sites = 22
Number in coding regions = 20
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 7

          **********

No masking
Map Score:   3.22176e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 8

          **********

No masking
Map Score:   3.22176e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 9

          **********

No masking
Map Score:   3.22176e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0